George Minadakis
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View article: Multi-omics dissection of Parkinson’s patients in subgroups associated with motor and cognitive severity
Multi-omics dissection of Parkinson’s patients in subgroups associated with motor and cognitive severity Open
Heterogeneity in the severity of Parkinson’s disease (PD) inhibits the effective interpretation of clinical trial outcomes. Multi-omics analysis may help explain the pathological mechanisms underlying disease progression and reveal biomark…
View article: Stage-specific gene pair ratios highlight genes and mechanisms related to presymptomatic and symptomatic Multiple Myeloma
Stage-specific gene pair ratios highlight genes and mechanisms related to presymptomatic and symptomatic Multiple Myeloma Open
We integrate the traditional analysis of DEGs with the concepts of MEGs and RMEGs, creating a novel computational approach capable of identifying key genes and pathways that can serve as a highly-filtered pool of candidate MM stage identif…
View article: Stage-specific gene ratios highlight genes and mechanisms related to presymptomatic and symptomatic Multiple Myeloma
Stage-specific gene ratios highlight genes and mechanisms related to presymptomatic and symptomatic Multiple Myeloma Open
Background/aim Multiple Myeloma is the second most common blood cancer, characterised by the accumulation of malignant plasma cells and the production of large amounts of a monoclonal immunoglobulin protein, in the bone marrow. The identif…
View article: PathIN: an integrated tool for the visualization of pathway interaction networks
PathIN: an integrated tool for the visualization of pathway interaction networks Open
PathIN is a web-service that provides an easy and flexible way for rapidly creating pathway-based networks at several functional biological levels: genes, compounds and reactions. The tool is supported by a database repository of reference…
View article: Vir2Drug: a drug repurposing framework based on protein similarities between pathogens
Vir2Drug: a drug repurposing framework based on protein similarities between pathogens Open
We draw from the assumption that similarities between pathogens at both pathogen protein and host protein level, may provide the appropriate framework to identify and rank candidate drugs to be used against a specific pathogen. Vir2Drug is…
View article: Bacterial Wars—a tool for the prediction of bacterial predominance based on network analysis measures
Bacterial Wars—a tool for the prediction of bacterial predominance based on network analysis measures Open
Bacterial Wars (BW) is a network-based tool that applies a two-step pipeline to display information on the competition of bacterial species found in the same microbiome. It utilizes antimicrobial peptide (AMP) sequence similarities to obta…
View article: Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19
Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19 Open
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is undeniably the most severe global health emergency since the 1918 Influenza outbreak. Depending on its evolutionary trajectory, the virus is expected to establish…
View article: Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains
Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains Open
This study aims to highlight SARS-COV-2 mutations which are associated with increased or decreased viral virulence. We utilize genetic data from all strains available from GISAID and countries’ regional information, such as deaths and case…
View article: PathExNET: A tool for extracting pathway expression networks from gene expression statistics
PathExNET: A tool for extracting pathway expression networks from gene expression statistics Open
A fundamental issue related to the understanding of the molecular mechanisms, is the way in which common pathways act across different biological experiments related to complex diseases. Using network-based approaches, this work aims to pr…
View article: Short-Term Foreshocks as Key Information for Mainshock Timing and Rupture: The Mw6.8 25 October 2018 Zakynthos Earthquake, Hellenic Subduction Zone
Short-Term Foreshocks as Key Information for Mainshock Timing and Rupture: The Mw6.8 25 October 2018 Zakynthos Earthquake, Hellenic Subduction Zone Open
Significant seismicity anomalies preceded the 25 October 2018 mainshock (Mw = 6.8), NW Hellenic Arc: a transient intermediate-term (~2 yrs) swarm and a short-term (last 6 months) cluster with typical time-size-space foreshock patterns: act…
View article: Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19
Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19 Open
The SARS-CoV-2 pandemic is undeniably the most severe global health emergency since the 1918 Influenza outbreak. Depending on its evolutionary trajectory, the virus is expected to establish itself as an endemic infectious respiratory disea…
View article: Analyzing Gene Expression Profiles from Ataxia and Spasticity Phenotypes to Reveal Spastic Ataxia Related Pathways
Analyzing Gene Expression Profiles from Ataxia and Spasticity Phenotypes to Reveal Spastic Ataxia Related Pathways Open
Spastic ataxia (SA) is a group of rare neurodegenerative diseases, characterized by mixed features of generalized ataxia and spasticity. The pathogenetic mechanisms that drive the development of the majority of these diseases remain unclea…
View article: Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains
Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains Open
This study aims to highlight SARS-COV-2 mutations which are associated with increased or decreased viral virulence. We utilize, genetic data from all strains available from GISAID and countries’ regional information such as deaths and case…
View article: PathWalks: identifying pathway communities using a disease-related map of integrated information
PathWalks: identifying pathway communities using a disease-related map of integrated information Open
Motivation Understanding the underlying biological mechanisms and respective interactions of a disease remains an elusive, time consuming and costly task. Computational methodologies that propose pathway/mechanism communities and reveal re…
View article: PathWalks: Identifying pathway communities using a disease-related map of integrated information
PathWalks: Identifying pathway communities using a disease-related map of integrated information Open
Understanding disease underlying biological mechanisms and respective interactions remains an elusive, time consuming and costly task. The realization of computational methodologies that can propose pathway/mechanism communities and reveal…
View article: ProtExA: A tool for post-processing proteomics data providing differential expression metrics, co-expression networks and functional analytics
ProtExA: A tool for post-processing proteomics data providing differential expression metrics, co-expression networks and functional analytics Open
ProTExA is a web-tool that provides a post-processing workflow for the analysis of protein and gene expression datasets. Using network-based bioinformatics approaches, ProTExA facilitates differential expression analysis and co-expression …
View article: Catamenial pneumothorax recurrence due to endometriosis
Catamenial pneumothorax recurrence due to endometriosis Open
Catamenial pneumothorax (CP) is considered to be the most common form of thoracic endometriosis syndrome, which also includes catamenial hemothorax, catamenial hemopneumothorax, catamenial hemoptysis, and endometriosis lung nodules. Diagno…
View article: Selecting variants of unknown significance through network-based gene-association significantly improves risk prediction for disease-control cohorts
Selecting variants of unknown significance through network-based gene-association significantly improves risk prediction for disease-control cohorts Open
View article: Inhibition of Breast Cancer Cell Invasion by Ras Suppressor-1 (RSU-1) Silencing Is Reversed by Growth Differentiation Factor-15 (GDF-15)
Inhibition of Breast Cancer Cell Invasion by Ras Suppressor-1 (RSU-1) Silencing Is Reversed by Growth Differentiation Factor-15 (GDF-15) Open
Extracellular matrix (ECM)-related adhesion proteins are important in metastasis. Ras suppressor-1 (RSU-1), a suppressor of Ras-transformation, is localized to cell–ECM adhesions where it interacts with the Particularly Interesting New Cys…
View article: A Web Tool for Ranking Candidate Drugs Against a Selected Disease Based on a Combination of Functional and Structural Criteria
A Web Tool for Ranking Candidate Drugs Against a Selected Disease Based on a Combination of Functional and Structural Criteria Open
View article: Revealing Clusters of Connected Pathways Through Multisource Data Integration in Huntington's Disease and Spastic Ataxia
Revealing Clusters of Connected Pathways Through Multisource Data Integration in Huntington's Disease and Spastic Ataxia Open
The advancement of scientific and medical research over the past years has generated a wealth of experimental data from multiple technologies, including genomics, transcriptomics, proteomics, and other forms of -omics data, which are avail…
View article: PathwayConnector: finding complementary pathways to enhance functional analysis
PathwayConnector: finding complementary pathways to enhance functional analysis Open
Summary PathwayConnector is a web-tool that facilitates the construction of complementary pathway-to-pathway networks and subnetworks of them, based on a reference pathway network derived from the rich information available either in KEGG …
View article: Integrating multi-source information on a single network to detect disease-related clusters of molecular mechanisms
Integrating multi-source information on a single network to detect disease-related clusters of molecular mechanisms Open
In this work we present an integration methodology, which aggregates a large number of the available data sources and types by exploiting the holistic nature of network approaches. It is simple, flexible and extendable generating solid con…
View article: Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches
Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches Open
Systems Bioinformatics is a relatively new approach, which lies in the intersection of systems biology and classical bioinformatics. It focuses on integrating information across different levels using a bottom-up approach as in systems bio…
View article: Foreshocks and short-term hazard assessment of large earthquakes usingcomplex networks: the case of the 2009 L'Aquila earthquake
Foreshocks and short-term hazard assessment of large earthquakes usingcomplex networks: the case of the 2009 L'Aquila earthquake Open
The monitoring of statistical network properties could be useful for the short-term hazard assessment of the occurrence of mainshocks in the presence of foreshocks. Using successive connections between events acquired from the earthquake c…
View article: Foreshocks and Short-Term Hazard Assessment to Large Earthquakes using Complex Networks: the Case of the 2009 L'Aquila Earthquake
Foreshocks and Short-Term Hazard Assessment to Large Earthquakes using Complex Networks: the Case of the 2009 L'Aquila Earthquake Open
The monitoring of statistical network properties could be useful for the short-term hazard assessment of the occurrence of mainshocks in the presence of foreshocks. Using successive connections between events acquired from the earthquake c…